remove other_patient_id and institute from sophia

Author: callachennault

import-scripts/update-sophia-mskimpact.sh

@@ -10,8 +10,8 @@ export SOPHIA_MSK_IMPACT_DATA_HOME="$SOPHIA_DATA_HOME/$COHORT_NAME"
 export SOPHIA_TMPDIR="$SOPHIA_MSK_IMPACT_DATA_HOME/tmp"
 
 # Patient and sample attributes that we want to deliver in our data
-DELIVERED_PATIENT_ATTRIBUTES="PATIENT_ID GENDER RACE ETHNICITY CURRENT_AGE_DEID STAGE_HIGHEST_RECORDED NUM_ICDO_DX ADRENAL_GLANDS BONE CNS_BRAIN INTRA_ABDOMINAL LIVER LUNG LYMPH_NODES OTHER PLEURA REPRODUCTIVE_ORGANS SMOKING_PREDICTIONS_3_CLASSES GLEASON_FIRST_REPORTED GLEASON_HIGHEST_REPORTED HISTORY_OF_PDL1 HISTORY_OF_D_MMR PRIOR_MED_TO_MSK YOST_INDEX_IMPUTED_MEDIAN OS_MONTHS OS_STATUS ECOG_KPS OTHER_PATIENT_ID PARTA_CONSENTED_12_245 PARTC_CONSENTED_12_245"
-DELIVERED_SAMPLE_ATTRIBUTES="SAMPLE_ID PATIENT_ID GLEASON_SAMPLE_LEVEL PDL1_POSITIVE CANCER_TYPE SAMPLE_TYPE SAMPLE_CLASS METASTATIC_SITE PRIMARY_SITE CANCER_TYPE_DETAILED GENE_PANEL SAMPLE_COVERAGE TUMOR_PURITY ONCOTREE_CODE MSI_COMMENT MSI_SCORE MSI_TYPE INSTITUTE SOMATIC_STATUS ARCHER CVR_TMB_COHORT_PERCENTILE CVR_TMB_SCORE CVR_TMB_TT_COHORT_PERCENTILE SEQ_DATE"
+DELIVERED_PATIENT_ATTRIBUTES="PATIENT_ID GENDER RACE ETHNICITY CURRENT_AGE_DEID STAGE_HIGHEST_RECORDED NUM_ICDO_DX ADRENAL_GLANDS BONE CNS_BRAIN INTRA_ABDOMINAL LIVER LUNG LYMPH_NODES OTHER PLEURA REPRODUCTIVE_ORGANS SMOKING_PREDICTIONS_3_CLASSES GLEASON_FIRST_REPORTED GLEASON_HIGHEST_REPORTED HISTORY_OF_PDL1 HISTORY_OF_D_MMR PRIOR_MED_TO_MSK YOST_INDEX_IMPUTED_MEDIAN OS_MONTHS OS_STATUS ECOG_KPS PARTA_CONSENTED_12_245 PARTC_CONSENTED_12_245"
+DELIVERED_SAMPLE_ATTRIBUTES="SAMPLE_ID PATIENT_ID GLEASON_SAMPLE_LEVEL PDL1_POSITIVE CANCER_TYPE SAMPLE_TYPE SAMPLE_CLASS METASTATIC_SITE PRIMARY_SITE CANCER_TYPE_DETAILED GENE_PANEL SAMPLE_COVERAGE TUMOR_PURITY ONCOTREE_CODE MSI_COMMENT MSI_SCORE MSI_TYPE SOMATIC_STATUS ARCHER CVR_TMB_COHORT_PERCENTILE CVR_TMB_SCORE CVR_TMB_TT_COHORT_PERCENTILE SEQ_DATE"
 
 # Duplicate columns that we want to filter out of MAF files
 MUTATIONS_EXTENDED_COLS_TO_FILTER="amino_acid_change,cdna_change,transcript,COMMENTS,Comments,comments,Matched_Norm_Sample_Barcode"